Conformational analysis of N-isopropylbenzohydroxamic acids: crystal structure, DFT, and NMR studies

X-ray crystal structure determinations together with density functional theory (DFT) calculations in vacuo and NMR studies in solution have been carried out for 4-MeOC₆H₄CONPrⁱOH 2a and 3,5-(NO₂)₂C₆H₃CONPrⁱOH 2b. The results were compared with that for the respective N-methyl benzohydroxamic acids. For crystal structures as well as for DFT-optimized geometries of 2 (both isomers) in vacuo, the effect of substituents in aromatic ring manifested by changing of charges is inconspicuous. Studies of potential energy surfaces showed that libration barrier around ω ₁ = 0° is low enough to make electron conjugation feasible, and that for 2b rotation barrier around C(O)N bond is higher by 6 kcal/mol and additionally, that rotation around N–C bond is hindered. A careful analysis of low-temperature ¹H NMR spectra confirmed the greater stability of Z-2a, the greater rigidity of E-2b and the influence of solvent on both isomers population. Despite solvent-dependent conformational alteration, both 2a and 2b crystallize exclusively as E isomers from ethyl acetate solution. Correlations of absolute ¹H, ¹³C, and ¹⁵N shielding calculations with experimental data were also analyzed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Electronic excitations of glycine, alanine, and cysteine conformers from first-principles calculations

The electronic and optical properties are studied for three conformers of amino acid molecules using gradient-corrected (spin-) density functional theory within a projector-augmented wave scheme and the supercell method. We investigate single-particle excitations such as ionization energies and electron affinities as well as pair excitations. By comparing eigenvalues resulting from several local and nonlocal energy functionals, the influence of treatment of exchange and correlation is demonstrated. The excitations are described within the Delta-self-consistent field method with an occupation number constraint to obtain excitation energies and Stokes shifts. The results are used to also discuss the optical absorption properties. In contrast to the lowest single- and two-particle excitation energies, remarkable changes are found in absorption spectra in dependence on the conformation of the molecule geometry.     

OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach

Density functional theory (B3LYP and BHandHLYP) and unrestricted second‐order Møller–Plesset (MP2) calculations have been performed using 3‐21G, 6‐31G(d,p), and 6‐311 G(2d,2p) basis sets, to study the OH hydrogen abstraction reaction from alanine and glycine. The structures of the different stationary points are discussed. Ring‐like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and very low or negative net energy barriers are obtained depending on the method and on the reacting site. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for B3LYP activation energies are included. A complex mechanism involving the formation of a prereactive complex is proposed, and the rate coefficients for the overall reactions are calculated using classical transition state theory. The predicted values of the rate coefficients are 3.54×10⁸ L?mol^?1?s^?1 for glycine and 1.38×10⁹ L?mol^?1?s^?1 for alanine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1138–1153, 2001     

Perfluorophenyl phosphonate analogues of aromatic amino acids: Synthesis,X-ray and DFT studies

Novel perfluorophenyl phosphonate analogues of phenylglycine and homophenylalanine were prepared in good to excellent yields, and subjected to solid state characterization by single-crystal X-ray diffraction analysis, and to investigations with the use of DFT methods.The α-aminophosphonates have a big potential for biological activity, and through S_NAr reactions may give an entrance to further structurally variable analogues of both amino acids.     

Novel dibenzosuberene substituted aroyl selenoureas: Synthesis,crystal structure,DFT, molecular docking and biological studies

Abstract

A series of aroyl selenourea dibenzosuberene (1–3) derivatives were synthesized and characterized by different analytical methods and single crystal X-ray crystallography. Quantum chemical computations were made using DFT to determine the structural and molecular properties of the compounds. The in vitro antibacterial action of the compounds was evaluated against chosen gram-negative (Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli), and gram-positive (Bacillus subtilis, Staphylococcus aureus, and Staphylococcus epidermidis) bacteria for their antifungal activity against Curvularia lunata, Penicillium notatum, and Aspergillus niger. Using molecular docking studies, the binding modes were understood along with the mechanism in opposing the target protein MurB.     

DFT studies of the structure, vibrational and NMR spectra of 2-amino-pyridine betaine monohydrate

Four of the most stable conformers of 2-amino-pyridine betaine (1-carboxymethyl-2-amino-pyridinium inner salt) monohydrates, 2-NH₂PB·H₂O, and one anhydrous were analyzed by the B3LYP/6-31G(d,p) calculations and compared with the X-ray data. Two types of optimized conformers can be distinguished: (a) with NH₂ and COO groups and (b) an imino tautomer with NH and COOH groups. A common feature of the optimized molecules are intramolecular hydrogen bonds between the COO⁻ and H₂N or COOH and HN groups. In the crystal both NH₂ and COO groups participate in intermolecular hydrogen bonds. The probable assignments of the anharmonic experimental solid state vibrational frequencies of 2-NH₂PB·H₂O and 2-ND₂PB·D₂O (conformer 2) based on the calculated B3LYP/6-31G(d,p) harmonic frequencies have been made. Correlations between experimental chemical shifts for 2-NH₂PB, its hydrochloride and 1-carboxyethyl-2-amino-pyridinium inner salt (¹³C and ¹H in D₂O) and GIAO/B3LYP/6-31G(d,p) calculated isotropic shielding constants, δ_exp=a+bσ_calc, are reported. Good linear regression between experimental and theoretical results for ¹³C was obtained. Only in 2-NH₂PB the hydrogen at -position is outside the linear correlation.     

A comparison of the results of PCILO andab initio SCF calculations for the molecules glycine,cysteine and N-acetyl-glycine

Conformational energy maps for glycine, cysteine and N-acetyl-glycine obtained using PCILO andab initio SCF calculations are compared.     

Synthesis,spectroscopy, X-ray crystal structure,and DFT studies on a platinum(II) Schiff-base complex

[PtCl₂(SMe₂)₂] reacts with (N,N′-bis(salicylidene)-1,2-cyclohexanediamine) to give (N,N′-bis(salicylidene)cyclohexane-1,2-diamine)platinum(II). The complex has been characterized by elemental analysis, infrared (IR), UV-Vis, and single-crystal X-ray diffraction. Pt(II) is in a square-planar environment, coordinated by a chelating N₂O₂ donor. Density functional theory (DFT) calculations such as geometry optimization, vibrational frequency, electronic properties, and natural bond orbital (NBO) have been performed for the platinum compound using the OLYP method at TZP(6-311G*) basis set. The optimization calculation shows that the geometry parameters can be reproduced with the OLYP/TZP basis set. Experimental IR frequencies and calculated vibrational frequencies support each other. Time-dependent DFT has been used for absorption wavelengths and results were compared with experimental data. Moreover, NBO analysis has been performed.     

Synthesis, characterization, crystal structure and DFT studies on 1',3'-dihydrospiro[fluorene-9,2'-perimidine

The title compound, 1′,3′-dihydrospiro[fluorene-9,2′-perimidine] has been synthesized and characterized by NMR, ESI-MS, IR, elemental analysis, UV–vis and fluorescence spectroscopy. The crystal structures of the title compound and its co-crsytal with 9-fluorenone have also been determined by X-ray single crystal diffraction. Density functional theory (DFT) calculations and vibrational frequencies have been performed at B3LYP/6-31G* level. The comparisons between the experimental vibrational frequencies and the predicted data show that B3LYP/6-31G* method can simulate the IR of the title compound on the whole. The theoretical electronic absorption spectra have been calculated by using TD-DFT method and compared with the experimental result. The solid-fluorescence determination of the title compound reveals two emission bans at 430 and 590 nm while its co-crystal reveals only one emission band at 590 nm.     

A highly distorted hexacoordinated silver(I) complex: synthesis,crystal structure,and DFT studies

A new highly distorted hexacoordinated silver(I) complex [AgL₂NO₃] with 2-(bis(methylthio)methylene)-1-phenylbutane-1,3-dione (L) as ligand is synthesized and characterized using elemental analysis, FTIR, NMR, and X-ray single-crystal structure analysis. The ligand (L) and the nitrate group act as bidentate ligands. The geometry around the silver ion has an intermediate configuration between a trigonal prism (TP) and an octahedron (OCT). Continuous shape measure (CShM) analysis indicated a closer configuration to TP than OCT. Experimentally and theoretically, the Ag–S bonds are shorter than any of the Ag–O bonds, indicating a stronger interaction between Ag⁺ (soft metal) and S-atom as a softer site than oxygen. Natural bond orbital (NBO) analyses showed higher interaction energies between the S-atom lone pairs and the Ag–antibonding NBO (8.61–31.39 kcal/mol) than LP(O)→Ag (3.48–11.46 kcal/mol). The acceptor antibonding NBO of the Ag atom has mainly s-orbital character. The Ag atom has a natural charge of +0.7579 e at the experimental structure, suggesting that negative charge was transferred from the ligand (0.0666 e) and nitrate (0.1090 e) to the Ag ion. Using Hirshfeld surface analysis, the important intermolecular interactions between molecular units within the crystal lattice of the ligand and its Ag-complex were analyzed and compared.     

Proton-transfer salts of diphenylphosphinic acid with substituted 2-aminopyridine: crystal structure,spectroscopic and DFT studies

Three proton-transfer salts of diphenylphosphinic acid (DPPA) with 2-amino-5-(X)-pyridine (AMPY, X = Cl, CN or CH₃), namely, 2-amino-5-chloropyridinium diphenylphosphinate, C₅H₆ClN₂⁺·C₁₂H₁₀O₂P⁻ ( 1 , X = Cl), 2-amino-5-cyanopyridinium diphenylphosphinate, C₆H₆N₃⁺·C₁₂H₁₀O₂P⁻ ( 2 , X = CN), and 2-amino-5-methylpyridinium diphenylphosphinate, C₆H₉N₂⁺·C₁₂H₁₀O₂P⁻ ( 3 , X = CH₃), have been synthesized and characterized by FT–IR and ¹H NMR spectroscopy, and X-ray crystallography. The crystal structures of compounds 1 – 3 were determined in the space group P for 1 and 2 , and C2/c for 3 . All three compounds contain N—H…O hydrogen-bonding interactions due to proton transfer from the O=P—OH group of DPPA as donor to the pyridine N atom of AMPY as acceptor. The proton transfer of compounds 1 – 3 was also verified by ¹H NMR and FT–IR spectroscopy. The stoichiometry of all three proton-transfer salts was determined to be 1:1 and the Benesi–Hildebrand equation was applied to determine the formation constant (K_CT) and the molar extinction coefficient (ϵ_CT) in each case. Theoretical density functional theory (DFT) calculations were performed to investigate the optimized geometries, the molecular electrostatic potentials (MEP) and the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) of all three proton-transfer salts. The results showed good agreement between the experimental data and the DFT computational analysis.     

Peptide models II. Intramolecular interactions and stable conformations of glycine,alanine, and valine peptide analogues

Summary The stable conformations of N and C protected amino acids of the type: HCONH-CHR-CONH₂ of glycine,l-alanine andl-valine have been obtained by fully optimizedab-initio computations with a 3–21G basis set. An original procedure has been devised to extract the side-chain/backbone interaction energy and the backbone and side-chain distortion energies. This enables us to analyze the stabilization/destabilization effects introduced by the side-chain in terms of electrostatic, induction and steric hindrance contributions.Dedicated to Dr. A. Pullman     

DFT studies of the structure and vibrational assignments of 4-hydroxy quinazoline and 2-hydroxy benzimidazole

The solid phase FT-IR and FT-Raman spectra of 4-hydroxy quinazoline and 2-hydroxy benzimidazole have been recorded in the regions 4000-400 and 3500-100 cm-1, respectively. Theoretical information on the optimised geometry, harmonic vibrational frequencies, infrared and Raman intensities were obtained by means of density functional theory using standard B3LYP/6-31G* level. This information was used in the assignment of the various fundamentals. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.     

Protonation of glycine and alanine: proton affinities, intrinsic basicities and proton transfer path

Proton affinities and intrinsic basicities for nitrogen and oxygen protonation in the gas phase of the amino acids glycine and alanine were calculated using density functional theory (DFT) and ab initio methods at different levels of theory from Hartree-Fock (HF) to G2 approximations. All methods gave good agreement for proton affinities for nitrogen protonation for both amino acids. However, dramatic differences were found between DFT, MP4//MP2, and G2 results on one hand, and MP4//HF results on the other to the calculation of structural and energetic characteristics of oxygen protonation in glycine and alanine. An investigation into the source of these differences revealed that electron correlation effects are chiefly responsible for the differences in calculated oxygen proton affinities between the various methods. It has been found that proton transfer between nitrogen and oxygen protonation sites in both amino acids occurs without a transfer path barrier when correlated methods were used to calculate the path energetics.     

Spectroscopic,structure, and DFT studies of cationic palladium(II) complexes with imidazole derivative ligands

Two palladium(II) complexes with imidazole derivative ligands have been synthesized. The molecular structures of the complexes were determined by X-ray crystallography and their spectroscopic properties were studied. Based on the crystal structures, computational investigations were carried out to determine the electronic structures of the complexes. The electronic spectra were calculated with use of time-dependent DFT method, and the transitions were correlated with the molecular orbitals of the complexes. The emission of the complex with 1-methylimidazole was examined.     

Synthesis,X-ray structure,DFT studies,and catalytic activity of a vanadium(V) complex containing a tridentate Schiff base

Reactions of a solution of NH₄VO₃ in H₂O₂ and water and salicylidene benzoyl hydrazine as a tridentate Schiff base (ONO) afford a six-coordinate V(V) complex [VO(ONO)(OCH₃)(CH₃OH)] with a distorted octahedral configuration. The complexes [VO(ONO)(OCH₃)(CH₃OH)] were isolated as air-stable crystalline solids and fully characterized, including by single-crystal X-ray structure analysis. DFT calculations have been performed to understand the electronic structure of the complex. Vibrational frequencies and maximum absorption wavelengths of the complex theoretically calculated are in good agreement with experimental values. [VO(ONO)(OCH₃)(CH₃OH)] shows efficient oxidation of sulfides to their corresponding sulfoxides using urea hydrogen peroxide as the oxidant at room temperature under air.     

Nickel(II) complex with an asymmetric tetradentate Schiff base ligand: synthesis,characterization, crystal structure,and DFT studies

Abstract

A new asymmetric tetradentate Schiff base, bis(5-methoxysalicylidene)-4-methylbenzene-1,2-diamine), H₂L, and its Ni(II) complex were prepared and characterized using elemental analyses (CHN), FTIR, UV–Vis, ¹H NMR, and ¹³C{¹H} NMR spectroscopic techniques, and crystal structures of both were determined by X-ray crystallography. For both ligand and Ni(II) complex, density functional theory calculations to find geometry parameters, IR frequencies, electronic properties, and natural bond orbital analysis (NBO) were done with M062X method and Def2-TZVP basis set. All calculated data are consistent with the experiments. NBO data for the Ni(II) complex show that the main type of transition in UV-Vis is interligand charge-transfer, which is assigned as π-π*.